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second pass base recalibration gatk4
I'm trying to run the second pass for the BaseRecalibrator with GATK4.
as seen in this post (https://gatkforums.broadinstitute.org/gatk/discussion/12985/how-to-do-a-second-pass-to-analyze-after-recalibration-in-gatk4) the previous
-BQSR was substituted with
-bqsr. also, it seems that there is no second pass available to do that?!
when I use it in:
GATK/gatk-18.104.22.168/gatk BaseRecalibrator \
-R CanFam3.1.dna.toplevel.fa \
-I sorted_WES_.bam \
--known-sites GATK/final.Axelsson.SNPs_nochr.vcf \
-bqsr recal.table \
I get indeed the error
"b is not a recognized option", suggesting that the option is not there..
however, the documentation here (https://software.broadinstitute.org/gatk/documentation/tooldocs/4.beta.4/org_broadinstitute_hellbender_tools_walkers_bqsr_AnalyzeCovariates.php) still says that you can run it.
--help there is no mention of the second pass and I'm confused about what I can/should do.
also, in previous versions I used
PrintReads with the recalibration table, while the first link above mentions
ApplyBQSR...so, which one is the one to use?